8000 Please change default MACS2 peak calling to narrow peak · Issue #403 · nf-core/atacseq · GitHub
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Please change default MACS2 peak calling to narrow peak #403

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SuhasSrinivasan opened this issue Jan 12, 2025 · 2 comments
8000
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Please change default MACS2 peak calling to narrow peak #403

SuhasSrinivasan opened this issue Jan 12, 2025 · 2 comments
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enhancement New feature or request

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@SuhasSrinivasan
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Description of feature

It would be very helpful if the default mode is changed to narrow peak, as most ATAC-seq analysis is centered around finding TFs and regulatory elements.
@SuhasSrinivasan SuhasSrinivasan added the enhancement New feature or request label Jan 12, 2025
@JoseEspinosa
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Not sure whether at this point this could be confusing for users and since this can be easily changed by using the corresponding parameter (--narrow_peak) maybe it would be better to keep it as it is.

@SuhasSrinivasan
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Thank you for reviewing.
Since the pipeline is meant for ATAC-seq specifically, it would be helpful to have --narrow_peak as default since that is the typical need.

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@JoseEspinosa @SuhasSrinivasan
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